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Which Option Do You Use With Breakdancer?

Which option do you use with Breakdancer ? I usually write no options like that 

perl bam2cfg.pl input.bam > input.cfg
breakdancer input.cfg > output.txt

I saw that some experts use the -g and -h options, I've read the readmefile and I still don't understand what difference does it make..

If you want to have CNV Gain AND Loss from paired-end sequencing which option would you use ?

ps : I'm a breakdancer newbee (>.<)

breakdancer cnv
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updated by Niek De Klein Niek De Klein • written by madkitty madkitty

1 answer

Read the usage page. It explains all the options. 

-g FILE   dump SVs and supporting reads in BED format for GBrowse
-h         print out Allele Frequency column, by default off
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written by Niek De Klein Niek De Klein

thanks but -h doesn't work for me it prints out an error message

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written by madkitty madkitty

If I just type in perl bam2cfg.pl -g -h myfile.bam > myfile.cfg

I have the following error : Use of uninitialized value in printf at bam2cfg.pl line 222.

I checked at line 222 and here is what I have : printf "%d",$flagHgram{$rg}{all};

I'm clueless..

• 0 views • link
written by madkitty madkitty

bam2cfg doesn't work without writing 'perl' before it. I think there's something to modify in the code of bam2cfg but I know nothing about perl .. Anyway Thanks

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written by madkitty madkitty

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